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In tropical forests, anthropogenic activities are major drivers of the destruction and degradation of natural habitats, causing severe biodiversity loss. African colobine monkeys (Colobinae) are mainly folivore and strictly arboreal primates that require large forests to subsist, being among the most vulnerable of all nonhuman primates. The Western red colobus Piliocolobus badius and the King colobus Colobus polykomos inhabit highly fragmented West African forests, including the Cantanhez Forests National Park (CFNP) in Guinea-Bissau. Both species are also found in the largest and best-preserved West African forest?the Taï National Park (TNP) in Ivory Coast. Colobine monkeys are hunted for bushmeat in both protected areas, but these exhibit contrasting levels of forest fragmentation, thus offering an excellent opportunity to investigate the importance of well-preserved forests for the maintenance of evolutionary potential in these arboreal primates. We estimated genetic diversity, population structure, and demographic history by using microsatellite loci and mitochondrial DNA. We then compared the genetic patterns of the colobines from TNP with the ones previously obtained for CFNP and found contrasting genetic patterns. Contrary to the colobines from CFNP that showed very low genetic diversity and a strong population decline, the populations in TNP still maintain high levels of genetic diversity and we found no clear signal of population decrease in Western red colobus and a limited decrease in King colobus. These results suggest larger and historically more stable populations in TNP compared to CFNP. We cannot exclude the possibility that the demographic effects resulting from the recent increase of bushmeat hunting are not yet detectable in TNP using genetic data. Nevertheless, the fact that the TNP colobus populations are highly genetically diverse and maintain large effective population sizes suggests that well-preserved forests are crucial for the maintenance of populations, species, and probably for the evolutionary potential in colobines.

Tree hollows provide shelters for a large number of forest-dependent vertebrate species worldwide. In Madagascar, where high historical and ongoing rates of deforestation and forest degradation are responsible for a major environmental crisis, reduced availability of tree hollows may lead to declines in hollow-dwelling species such as sportive lemurs, one of the most species-rich groups of lemurs. The identification of native tree species used by hollow-dwelling lemurs may facilitate targeted management interventions to maintain or improve habitat quality for these lemurs. During an extensive survey of sportive lemurs in northern Madagascar, we identified one tree species, Strychnos madagascariensis (Loganiaceae), the spineless monkey orange tree, as a principal sleeping site of two species of northern sportive lemurs, Lepilemur ankaranensis and L. milanoii (Lepilemuridae). This tree species represented 32.5% (n=150) of the 458 sleeping sites recorded. This result suggests that S. madagascariensis may be valuable for the conservation of hollow-dwelling lemurs. De nombreux vertébrés forestiers à travers le monde trouvent refuge dans des cavités et des trous d’arbres. À Madagascar, les taux de déforestation historiques et actuels sont responsables d’une crise environnementale majeure. Dans ce contexte, une disponibilité réduite d’arbres pourvus de cavités pourrait entrainer le déclin des espèces dépendant de ces abris comme par exemple les lépilemurs, un des groupes de lémuriens les plus riches en espèces. L’identification des espèces d’arbres indigènes creusés de trous et utilisés par les lémuriens pourrait faciliter la mise en place d’actions de conservation ayant pour but de maintenir ou améliorer l’habitat de ces lémuriens. Au cours d’une étude réalisée dans le Nord de Madagascar, nous avons observé que Strychnos madagascariensis (Loganiaceae) était fréquemment utilisé comme site dortoir par les deux espèces de lépilemurs présentes, Lepilemur ankaranensis and L. milanoii (Lepilemuridae). Cette espèce d’arbre concernait 32,5% (n = 150) des 458 sites dortoirs enregistrés. Ce résultat suggère que S. madagascariensis pourrait être important pour la conservation des lémuriens dépendant de sites dortoirs.

La région Loky-Manambato dans le Nord de Madagascar, est connue pour abriter le propithèque à couronne dorée (Propithecus tattersalli), un lémurien emblématique et endémique de la région. Néanmoins cette région composée d’une dizaine de fragments forestiers de taille moyenne et encore relativement peu étudiés, abrite aussi le microcèbe roux du nord (Microcebus tavaratra). Malgré la gestion des forêts de cette région par l’ONG Fanamby depuis 2005, aucune étude n’avait encore été menée dans chacun des fragments forestiers de la région pour déterminer la présence et quantifier la taille des populations de microcèbes de chacun d’entre eux. Lors de notre étude nous avons tenté d’estimer les densités et les tailles des populations de M. tavaratra dans neuf des dix principaux fragments forestiers de la région. Dans ce but nous avons utilisé la méthode de «line transect distance-sampling». Nos résultats montrent que les densités de microcèbes sont relativement élevées, et varient de 28 à 325 ind/km² entre fragments forestiers de la région. Desétudes plus approfondies des données collectées seront nécessaires pour déterminer les variables environnementales responsables des différences de densité observées. FCT grant: (SFRH/BD/64875/2009); l’Institut Français de la Biodiversité, GDRI Madagascar, “Laboratoire d’Excellence” (LABEX) TULIP: (ANR -10-LABX-41).

Most species do not live in a constant environment over space or time. Their environment is often heterogeneous with a huge variability in resource availability and exposure to pathogens or predators, which may affect the local densities of the species. Moreover, the habitat might be fragmented, preventing free and isotropic migrations between local sub-populations (demes) of a species, making some demes more isolated than others. For example, during the last ice age populations of many species migrated towards refuge areas from which re-colonization originated when conditions improved. However, populations that could not move fast enough or could not adapt to the new environmental conditions faced extinctions. Populations living in these types of dynamic environments are often referred to as metapopulations and modeled as an array of subdivisions (or demes) that exchange migrants with their neighbors. Several studies have focused on the description of their demography, probability of extinction and expected patterns of diversity at different scales. Importantly, all these evolutionary processes may affect genetic diversity, which can affect the chance of populations to persist. In this chapter we provide an overview on the consequences of fragmentation, long-distance dispersal, range contractions and range shifts on genetic diversity. In addition, we describe new methods to detect and quantify underlying evolutionary processes from sampled genetic data. Laboratoire d’Excellence (LABEX) entitled TULIP: (ANR-10-LABX-41).

Avahi laniger est le seul lémurien nocturne appartenant à la famille des Indriidae qui habite les forêts humides de l’est de Madagascar (Mittermeier et. al., 2010) dont une partie disparaît chaque année (exploitation du bois, pratique du «tavy» ou culture sur brûlis) (Beaucent and Fayolle, 2011; Lehman and Wright, 2000). La fragmentation et la destruction de leur habitat ainsi que la chasse menacent la survie de nombreuses espèces de lémuriens incluant celle de A. laniger (Jenkins et. al., 2011; Rakotondravony and Rabenandrasana, 2011; Anderson, Rowcliffe and Cowlishaw, 2007). Nous avons réalisé, entre fin Avril et Mai 2012, une étude de densité de la population de A. laniger au sein de l’aire protégée de Manompana-Ambodiriana afin d’estimer la taille de la population totale et de déterminer l’impact du projet de conservation menée par l’Association de Défense de la Forêt d’Ambodiriana (ADEFA) qui recherche l’évolution démographique à moyen terme de cette espèce. "LABEX" TULIP: (ANR-10-LABX-41), fct fellowship: (SFRH/BD/64875/2009).

Propithecus perrieri (Perrier’s sifaka) is one of the most endangered lemur species due to its small and fragmented distribution range. Despite a Critically Endangered (CR) conservation and flagship species status, there are still many uncertainties regarding its actual distribution and its presence in some forests of its putative distribution range. We report the results of diurnal and nocturnal surveys carried out in 2012 across most forest fragments of its putative distribution range, namely the Ankarana National Park, the Analamerana Special Reserve and Andrafiamena-Andava-koera Protected Area. During our surveys the species was only observed in Andrafiamena and Analamerana protected areas. FCT fellowship: (SFRH/BD/64875/2009), Institut Français de la Biodiversité, the GDRI Madagascar, the “Laboratoire d'Excellence” (LABEX) entitled TULIP (ANR-10-LABX-41), Instituto Gulbenkian de Ciência, “Optimus Alive!” Biodiversity grant, The Rufford Small Grant for Nature Conservation: (ref. 10941-1), Département de Biologie Animale et Ecologie (D.B.A.E.), Faculté des Sciences, University of Mahajanga, the University of Antsiranana, and the Fanamby NGO (in particular S. Rajaobelina), Madagascar National Park, Analamerana Special Reserve, Ankarana National Park.

Habitat fragmentation may strongly reduce individuals' dispersal among resource patches and hence influence population distribution and persistence. We studied the impact of landscape heterogeneity on the dispersal of the golden-crowned sifaka (Propithecus tattersalli), an endangered social lemur species living in a restricted and highly fragmented landscape. We combined spatial analysis and population genetics methods to describe population units and identify the environmental factors which best predict the rates and patterns of genetic differentiation within and between populations. We used non-invasive methods to genotype 230 individuals at 13 microsatellites in all the main forest fragments of its entire distribution area. Our analyses suggest that the Manankolana River and geographical distance are the primary structuring factors, while a national road crossing the region does not seem to impede gene flow. Altogether, our results are in agreement with a limited influence of forest habitat connectivity on gene flow patterns (except for North of the species' range), suggesting that dispersal is still possible today among most forest patches for this species. Within forest patches, we find that dispersal is mainly among neighbouring social groups, hence confirming previous behavioural observations

Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model-based inference in population genetics.

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Genetic variability of fifty-five shark specimens from the genus Carcharhinus was analysed using 18 allozyme loci. Sixteen loci were polymorphic either within, or between, species. Levels of genetic polymorphism, as measured by observed heterozygosity values, ranged from 0.008 (±0.008) to 0.056 (±0.038). Nei’s (1978) genetic distances between Carcharhinus species ranged from 0.235 to 0.784. Morphological identification, using keys, classified them as members of four morphological groups, corresponding to four species: Carcharhinus signatus, C. brevipinna, C. longimanus and C. limbatus. Genetic data confirmed that the first three species were correctly identified, but that the C. limbatus individuals could be further divided into two clearly-differentiated groups, one of which is probably C. limbatus, whereas the other could either be misidentified or be a new taxon.

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La génétique des organismes marins a longtemps souffert du manque de confiance des gestionnaires des pêches par l'absence de résultats spectaculaires. Nous avons analysé la variabilité génétique de deux espèces de sardinelles (#Sardinella aurita$ et #S. maderensis$) par l'intermédiaire de sa variabilité allozymique. Nous n'avons pas trouvé de variabilité suffisante chez #S. aurita$ pour pouvoir conclure sur sa structuration génétique. En revanche #S. maderensis$ s'est révélée plus variable. Nous avons donc pu chercher à mettre en évidence sa différenciation génétique sur son aire de répartition. La valeur de l'indice Fst de WRIGHT estimé selon WEIR et COCKERHAM (1984) s'est révélée faible (Fst = 0.0085) mais significativement différente de zéro (c'est-à-dire de la panmixie). Une différenciation génétique existe donc pour #S. maderensis$. Cette différenciation génétique est donc également dynamique. (D'après résumé d'auteur)